Development and Application of Tools for Genetic Analysis of Clonal Populations PublicDeposited

Descriptions

Research on the population genetics of microbial organisms requires the use of specialized analyses designed for clonal organisms to avoid violating the assumptions of traditional population genetic models. The tools necessary for performing these analyses existed as a set of unrelated software with non-overlapping capabilities and did not cover all aspects of analysis. This meant that researchers not only had to reshape their data into different formats for each analysis, but they also had to switch computing platforms, thus creating a drain in time, and increasing the risk of propagating human error into the analysis. To address this problem, we created the software package poppr, written in the R statistical language, available on all computing platforms. This package is designed for analysis of clonal, partially clonal, and sexual populations, empowering researchers to perform their work in a reproducible manner. We additionally demonstrate the utility of poppr for both plant pathological and theoretical questions by using real-world and simulated data. In chapter 4, we apply these new tools to demonstrate evidence for at least two origins for the outbreak of the Sudden Oak Death pathogen, Phytophthora ramorum in Curry County, Oregon. In chapter 5, we use poppr to assess the power of the index of association with clone-correction, showing that clone-correction has the potential to reduce the power of detecting clonal reproduction. All of the software and analyses in this work were performed in an open and reproducible framework, serving as an example of the power of reproducible research in plant pathology.